BN0329 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 4.5813e-05 3.6882e-04
Layer 6 1.5187e-04 3.1786e-03
Layer 3 2.1754e-04 3.8000e-03
Layer 2 1.3073e-03 5.3742e-02
Layer 1 6.4653e-03 5.0384e-02
WM 9.3340e-03 1.2356e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 1.8164 0.6260
NEUROD2 Layer 5 2.4727 0.6071
STMN2 Layer 5 2.5840 0.6047
CELF4 Layer 5 2.6660 0.6024
SLC17A7 Layer 6 2.4209 0.5893
SNAP25 Layer 5 2.8906 0.5859
TUBA1B Layer 5 2.6426 0.5765
SYT1 Layer 5 2.6455 0.5749
ZBTB7A Layer 3 2.2832 0.5716
ARL2 Layer 5 2.1543 0.5660
CALM3 Layer 2 2.3281 0.5655
ENO2 Layer 5 2.3125 0.5644
SPOCK1 Layer 6 2.3086 0.5615
UCHL1 Layer 5 2.5664 0.5592
NRGN Layer 5 2.3750 0.5557
BASP1 Layer 5 2.5449 0.5555
NAPB Layer 5 2.4512 0.5549
PGRMC1 Layer 5 2.1543 0.5542
GNAO1 Layer 6 2.4297 0.5526
NEFM Layer 5 2.5215 0.5526
LMO4 Layer 5 2.3242 0.5520
YWHAB Layer 5 2.5391 0.5515
HSP90AB1 Layer 5 2.3809 0.5499
THY1 Layer 6 2.3340 0.5493
MAP2 Layer 5 2.2715 0.5492
TPI1 Layer 5 2.4883 0.5489
RTN3 Layer 5 2.7246 0.5483
MTCH1 Layer 5 2.2969 0.5483
RAB6B Layer 5 2.3896 0.5477
SH3GL2 Layer 5 2.1123 0.5467
YWHAH Layer 3 2.3555 0.5453
VAMP2 Layer 5 2.6104 0.5444
TMSB10 Layer 5 2.4570 0.5440
SEZ6L2 Layer 5 2.4102 0.5433
ATP6V0A1 Layer 5 2.2715 0.5432
ANK2 Layer 5 2.5059 0.5384
GPI Layer 5 2.2832 0.5372
DNM1 Layer 5 2.6455 0.5365
RTN1 Layer 5 2.4258 0.5345
SPTBN1 Layer 5 2.3652 0.5320
PPP2R1A Layer 5 2.3184 0.5285
NORAD Layer 6 2.2324 0.5263
RPS3 Layer 5 2.4844 0.5255
CLSTN1 Layer 5 2.2461 0.5233
NEFL Layer 5 2.7070 0.5225
NDUFA4 Layer 3 2.2422 0.5220
KLC1 Layer 5 2.3730 0.5219
STMN1 Layer 5 2.6221 0.5195
SSTR2 Layer 5 2.2295 0.5193
ATP6V0C Layer 5 2.3438 0.5183

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0329
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0329_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0329/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0329/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0329/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0329/report/PD/BN0329_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0329/report/PD/BN0329_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 23:32:34
  • Number of Processes: 10
  • Spending Time: 0h 2m